#include  <stdio.h>
#include <string.h>
#include <math.h>  

#include <nicklib.h>
#include <getpars.h> 

int verbose = NO ;
double nval = -1 ;

char *iname = NULL ;
char *parname = NULL ;
char *oname = NULL ;

char *twxtab = NULL ;

/**
The Broad Institute
SOFTWARE COPYRIGHT NOTICE AGREEMENT
This software and its documentation are copyright <2006> by the
Broad Institute/Massachusetts Institute of Technology. All rights are
reserved.

This software is supplied without any warranty or guaranteed support
whatsoever. Neither the Broad Institute nor MIT can be responsible for
its use, misuse, or functionality.
*/

void readcommands(int argc, char **argv) ;

#define VERSION    "1000"  

int  minleneig = 10 ;


int   
main  (int argc , char **argv) 
{
   int mx, nx ;
   FILE *ifile, *ofile ;
   int nlambda = 0 ;
   int i, m ;
   double zn, zvar, tw, tail ;
   double *xx[0], *lambda ;

   readcommands(argc, argv) ;
   settwxtable(twxtab) ;

   if (oname == NULL) ofile = stdout ; 
   else openit(oname, &ofile, "w") ;

   if (iname==NULL) fatalx("i paraameter compulsory\n") ;
   nlambda = numlines(iname) ;
   ZALLOC(lambda, nlambda, double) ;
   xx[0] = lambda ;
   nlambda = getxx(xx, nlambda, 1, iname) ;
   vst(lambda, lambda, -1.0, nlambda) ;
   sortit(lambda, NULL,  nlambda) ;
   vst(lambda, lambda, -1.0, nlambda) ;
   m = numgtz(lambda, nlambda) ;

   fprintf(ofile,"%4s  %12s", "#N", "eigenvalue") ;
   fprintf(ofile,"%12s",  "difference") ;
   fprintf(ofile," %9s %12s", "twstat", "p-value") ;
   fprintf(ofile," %9s", "effect. n") ;
   fprintf(ofile,"\n");

   for (i=0; i<m; ++i) { 

    zn = nval ;
    tail = dotwcalc(lambda+i, m-i, &tw, &zn, &zvar, minleneig) ;
    fprintf(ofile,"%4d  %12.6f", i+1, lambda[i]) ;
    if (i==0) fprintf(ofile, "%12s", "NA") ;
    else fprintf(ofile,"%12.6f", lambda[i]-lambda[i-1]) ;
    if (tail>=0.0) fprintf(ofile, " %9.3f %12.6g", tw, tail) ;
    else fprintf(ofile, " %9s %12s", "NA", "NA") ;
   if (zn>0.0) {
    fprintf(ofile, " %9.3f", zn) ;
   }
   else  {
    fprintf(ofile, " %9s", "NA") ;
   }
    fprintf(ofile, "\n") ;
  }
}

void readcommands(int argc, char **argv) 
{

  int i ;
  char *parname = NULL ;
  phandle *ph ;
  char str[5000]  ;
  char *tempname ;
  int n ;

  while ((i = getopt (argc, argv, "i:o:p:n:m:t:V")) != -1) {

    switch (i)
      {

      case 'i':
	iname = strdup(optarg) ;
	break;

      case 'o':
	oname = strdup(optarg) ;
	break;

      case 't':
	twxtab  = strdup(optarg) ;
	break;

      case 'n':
	nval = atof(optarg) ;
	break;

      case 'm':
	minleneig = atoi(optarg) ;
	break;

      case 'p':
	parname = strdup(optarg) ;
	break;

      case 'V':
	verbose = YES ;
	break; 

      case '?':
	printf ("Usage: bad params.... \n") ;
	fatalx("bad params\n") ;
      }
  }

   if (parname == NULL) return ;

   printf("parameter file: %s\n", parname) ;
   ph = openpars(parname) ;

   getstring(ph, "input:", &iname) ;
   getstring(ph, "output:", &oname) ;
   getdbl(ph, "nval:", &nval) ;
   getint(ph, "minleneig:", &minleneig) ;

   writepars(ph);
   closepars(ph) ;

}

